Starting phenix.real_space_refine on Thu Jun 12 17:44:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8i48_35164/06_2025/8i48_35164.cif Found real_map, /net/cci-nas-00/data/ceres_data/8i48_35164/06_2025/8i48_35164.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.74 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8i48_35164/06_2025/8i48_35164.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8i48_35164/06_2025/8i48_35164.map" model { file = "/net/cci-nas-00/data/ceres_data/8i48_35164/06_2025/8i48_35164.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8i48_35164/06_2025/8i48_35164.cif" } resolution = 2.74 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 40 5.49 5 S 20 5.16 5 Cl 5 4.86 5 C 9380 2.51 5 N 2070 2.21 5 O 2755 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 14270 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "C" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "D" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "B" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "E" Number of atoms: 2540 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} Conformer: "B" Number of residues, atoms: 312, 2529 Classifications: {'peptide': 312} Link IDs: {'PTRANS': 18, 'TRANS': 293} bond proxies already assigned to first conformer: 2585 Chain: "A" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "C" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "D" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "B" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "E" Number of atoms: 282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 282 Unusual residues: {' CL': 1, 'PEE': 8} Classifications: {'undetermined': 9} Link IDs: {None: 8} Unresolved non-hydrogen bonds: 127 Unresolved non-hydrogen angles: 127 Unresolved non-hydrogen dihedrals: 133 Chain: "A" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "D" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "B" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Chain: "E" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 32 Classifications: {'water': 32} Link IDs: {None: 31} Residues with excluded nonbonded symmetry interactions: 5 residue: pdb=" N AARG A 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG A 293 " occ=0.47 residue: pdb=" N AARG C 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG C 293 " occ=0.47 residue: pdb=" N AARG D 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG D 293 " occ=0.47 residue: pdb=" N AARG B 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG B 293 " occ=0.47 residue: pdb=" N AARG E 293 " occ=0.53 ... (20 atoms not shown) pdb=" NH2BARG E 293 " occ=0.47 Time building chain proxies: 14.20, per 1000 atoms: 1.00 Number of scatterers: 14270 At special positions: 0 Unit cell: (94.24, 93.48, 123.12, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 5 17.00 S 20 16.00 P 40 15.00 O 2755 8.00 N 2070 7.00 C 9380 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.44 Conformation dependent library (CDL) restraints added in 2.7 seconds 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3060 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 20 sheets defined 34.3% alpha, 34.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.28 Creating SS restraints... Processing helix chain 'A' and resid 118 through 121 Processing helix chain 'A' and resid 196 through 212 removed outlier: 5.319A pdb=" N LEU A 203 " --> pdb=" O PRO A 199 " (cutoff:3.500A) Proline residue: A 204 - end of helix removed outlier: 3.629A pdb=" N SER A 212 " --> pdb=" O ILE A 208 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 243 Processing helix chain 'A' and resid 253 through 282 Processing helix chain 'A' and resid 284 through 315 removed outlier: 3.532A pdb=" N ALA A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N ILE A 297 " --> pdb=" O AARG A 293 " (cutoff:3.500A) Proline residue: A 300 - end of helix Processing helix chain 'C' and resid 118 through 121 Processing helix chain 'C' and resid 196 through 212 removed outlier: 5.319A pdb=" N LEU C 203 " --> pdb=" O PRO C 199 " (cutoff:3.500A) Proline residue: C 204 - end of helix removed outlier: 3.630A pdb=" N SER C 212 " --> pdb=" O ILE C 208 " (cutoff:3.500A) Processing helix chain 'C' and resid 220 through 243 Processing helix chain 'C' and resid 253 through 282 Processing helix chain 'C' and resid 284 through 315 removed outlier: 3.532A pdb=" N ALA C 288 " --> pdb=" O GLN C 284 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ILE C 297 " --> pdb=" O AARG C 293 " (cutoff:3.500A) Proline residue: C 300 - end of helix Processing helix chain 'D' and resid 118 through 121 Processing helix chain 'D' and resid 196 through 212 removed outlier: 5.320A pdb=" N LEU D 203 " --> pdb=" O PRO D 199 " (cutoff:3.500A) Proline residue: D 204 - end of helix removed outlier: 3.630A pdb=" N SER D 212 " --> pdb=" O ILE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 220 through 243 Processing helix chain 'D' and resid 253 through 282 Processing helix chain 'D' and resid 284 through 315 removed outlier: 3.533A pdb=" N ALA D 288 " --> pdb=" O GLN D 284 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE D 297 " --> pdb=" O AARG D 293 " (cutoff:3.500A) Proline residue: D 300 - end of helix Processing helix chain 'B' and resid 118 through 121 Processing helix chain 'B' and resid 196 through 212 removed outlier: 5.320A pdb=" N LEU B 203 " --> pdb=" O PRO B 199 " (cutoff:3.500A) Proline residue: B 204 - end of helix removed outlier: 3.630A pdb=" N SER B 212 " --> pdb=" O ILE B 208 " (cutoff:3.500A) Processing helix chain 'B' and resid 220 through 243 Processing helix chain 'B' and resid 253 through 282 Processing helix chain 'B' and resid 284 through 315 removed outlier: 3.533A pdb=" N ALA B 288 " --> pdb=" O GLN B 284 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ILE B 297 " --> pdb=" O AARG B 293 " (cutoff:3.500A) Proline residue: B 300 - end of helix Processing helix chain 'E' and resid 118 through 121 Processing helix chain 'E' and resid 196 through 212 removed outlier: 5.319A pdb=" N LEU E 203 " --> pdb=" O PRO E 199 " (cutoff:3.500A) Proline residue: E 204 - end of helix removed outlier: 3.630A pdb=" N SER E 212 " --> pdb=" O ILE E 208 " (cutoff:3.500A) Processing helix chain 'E' and resid 220 through 243 Processing helix chain 'E' and resid 253 through 282 Processing helix chain 'E' and resid 284 through 315 removed outlier: 3.532A pdb=" N ALA E 288 " --> pdb=" O GLN E 284 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N ILE E 297 " --> pdb=" O AARG E 293 " (cutoff:3.500A) Proline residue: E 300 - end of helix Processing sheet with id=AA1, first strand: chain 'A' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU A 45 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 23 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS A 48 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR A 17 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU A 45 " --> pdb=" O TYR A 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS A 38 " --> pdb=" O CYS A 27 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N CYS A 27 " --> pdb=" O LYS A 38 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN A 40 " --> pdb=" O ILE A 25 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N TYR A 23 " --> pdb=" O PHE A 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS A 48 " --> pdb=" O THR A 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR A 17 " --> pdb=" O LYS A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 76 through 78 removed outlier: 6.664A pdb=" N ASP A 185 " --> pdb=" O ALA A 167 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA A 167 " --> pdb=" O ASP A 185 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN A 187 " --> pdb=" O PHE A 165 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE A 165 " --> pdb=" O GLN A 187 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N ARG A 189 " --> pdb=" O GLU A 163 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 174 through 176 Processing sheet with id=AA5, first strand: chain 'C' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU C 45 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 23 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS C 48 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR C 17 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU C 45 " --> pdb=" O TYR C 102 " (cutoff:3.500A) removed outlier: 7.222A pdb=" N LYS C 38 " --> pdb=" O CYS C 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS C 27 " --> pdb=" O LYS C 38 " (cutoff:3.500A) removed outlier: 7.034A pdb=" N ASN C 40 " --> pdb=" O ILE C 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR C 23 " --> pdb=" O PHE C 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS C 48 " --> pdb=" O THR C 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR C 17 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 76 through 78 removed outlier: 6.666A pdb=" N ASP C 185 " --> pdb=" O ALA C 167 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA C 167 " --> pdb=" O ASP C 185 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN C 187 " --> pdb=" O PHE C 165 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE C 165 " --> pdb=" O GLN C 187 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG C 189 " --> pdb=" O GLU C 163 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 174 through 176 Processing sheet with id=AA9, first strand: chain 'D' and resid 99 through 111 removed outlier: 3.668A pdb=" N LEU D 45 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 23 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS D 48 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR D 17 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 99 through 111 removed outlier: 3.668A pdb=" N LEU D 45 " --> pdb=" O TYR D 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS D 38 " --> pdb=" O CYS D 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS D 27 " --> pdb=" O LYS D 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN D 40 " --> pdb=" O ILE D 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR D 23 " --> pdb=" O PHE D 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS D 48 " --> pdb=" O THR D 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR D 17 " --> pdb=" O LYS D 48 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 76 through 78 removed outlier: 6.666A pdb=" N ASP D 185 " --> pdb=" O ALA D 167 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N ALA D 167 " --> pdb=" O ASP D 185 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN D 187 " --> pdb=" O PHE D 165 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE D 165 " --> pdb=" O GLN D 187 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG D 189 " --> pdb=" O GLU D 163 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 174 through 176 Processing sheet with id=AB4, first strand: chain 'B' and resid 99 through 111 removed outlier: 3.668A pdb=" N LEU B 45 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 23 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS B 48 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR B 17 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 99 through 111 removed outlier: 3.668A pdb=" N LEU B 45 " --> pdb=" O TYR B 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS B 38 " --> pdb=" O CYS B 27 " (cutoff:3.500A) removed outlier: 5.121A pdb=" N CYS B 27 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN B 40 " --> pdb=" O ILE B 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR B 23 " --> pdb=" O PHE B 42 " (cutoff:3.500A) removed outlier: 4.632A pdb=" N LYS B 48 " --> pdb=" O THR B 17 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N THR B 17 " --> pdb=" O LYS B 48 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'B' and resid 76 through 78 removed outlier: 6.665A pdb=" N ASP B 185 " --> pdb=" O ALA B 167 " (cutoff:3.500A) removed outlier: 4.539A pdb=" N ALA B 167 " --> pdb=" O ASP B 185 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N GLN B 187 " --> pdb=" O PHE B 165 " (cutoff:3.500A) removed outlier: 4.359A pdb=" N PHE B 165 " --> pdb=" O GLN B 187 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG B 189 " --> pdb=" O GLU B 163 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 174 through 176 Processing sheet with id=AB8, first strand: chain 'E' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU E 45 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E 23 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS E 48 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR E 17 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 99 through 111 removed outlier: 3.669A pdb=" N LEU E 45 " --> pdb=" O TYR E 102 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N LYS E 38 " --> pdb=" O CYS E 27 " (cutoff:3.500A) removed outlier: 5.120A pdb=" N CYS E 27 " --> pdb=" O LYS E 38 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ASN E 40 " --> pdb=" O ILE E 25 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N TYR E 23 " --> pdb=" O PHE E 42 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N LYS E 48 " --> pdb=" O THR E 17 " (cutoff:3.500A) removed outlier: 6.232A pdb=" N THR E 17 " --> pdb=" O LYS E 48 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'E' and resid 76 through 78 removed outlier: 6.666A pdb=" N ASP E 185 " --> pdb=" O ALA E 167 " (cutoff:3.500A) removed outlier: 4.540A pdb=" N ALA E 167 " --> pdb=" O ASP E 185 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N GLN E 187 " --> pdb=" O PHE E 165 " (cutoff:3.500A) removed outlier: 4.358A pdb=" N PHE E 165 " --> pdb=" O GLN E 187 " (cutoff:3.500A) removed outlier: 6.791A pdb=" N ARG E 189 " --> pdb=" O GLU E 163 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'E' and resid 174 through 176 680 hydrogen bonds defined for protein. 1985 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 4.35 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2220 1.32 - 1.45: 3768 1.45 - 1.57: 8307 1.57 - 1.69: 80 1.69 - 1.81: 35 Bond restraints: 14410 Sorted by residual: bond pdb=" CG ASN B 83 " pdb=" ND2 ASN B 83 " ideal model delta sigma weight residual 1.328 1.377 -0.049 2.10e-02 2.27e+03 5.34e+00 bond pdb=" CG ASN E 83 " pdb=" ND2 ASN E 83 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.30e+00 bond pdb=" CG ASN A 83 " pdb=" ND2 ASN A 83 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.19e+00 bond pdb=" CG ASN C 83 " pdb=" ND2 ASN C 83 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.16e+00 bond pdb=" CG ASN D 83 " pdb=" ND2 ASN D 83 " ideal model delta sigma weight residual 1.328 1.376 -0.048 2.10e-02 2.27e+03 5.14e+00 ... (remaining 14405 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.95: 18607 1.95 - 3.89: 646 3.89 - 5.84: 127 5.84 - 7.78: 5 7.78 - 9.73: 15 Bond angle restraints: 19400 Sorted by residual: angle pdb=" C GLU C 35 " pdb=" N THR C 36 " pdb=" CA THR C 36 " ideal model delta sigma weight residual 123.27 116.49 6.78 1.85e+00 2.92e-01 1.34e+01 angle pdb=" C GLU A 35 " pdb=" N THR A 36 " pdb=" CA THR A 36 " ideal model delta sigma weight residual 123.27 116.50 6.77 1.85e+00 2.92e-01 1.34e+01 angle pdb=" C GLU D 35 " pdb=" N THR D 36 " pdb=" CA THR D 36 " ideal model delta sigma weight residual 123.27 116.51 6.76 1.85e+00 2.92e-01 1.34e+01 angle pdb=" C GLU B 35 " pdb=" N THR B 36 " pdb=" CA THR B 36 " ideal model delta sigma weight residual 123.27 116.51 6.76 1.85e+00 2.92e-01 1.33e+01 angle pdb=" C GLU E 35 " pdb=" N THR E 36 " pdb=" CA THR E 36 " ideal model delta sigma weight residual 123.27 116.52 6.75 1.85e+00 2.92e-01 1.33e+01 ... (remaining 19395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.34: 8340 32.34 - 64.68: 460 64.68 - 97.02: 45 97.02 - 129.36: 30 129.36 - 161.70: 40 Dihedral angle restraints: 8915 sinusoidal: 4215 harmonic: 4700 Sorted by residual: dihedral pdb=" CA ARG D 118 " pdb=" C ARG D 118 " pdb=" N TYR D 119 " pdb=" CA TYR D 119 " ideal model delta harmonic sigma weight residual 180.00 -154.82 -25.18 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA ARG B 118 " pdb=" C ARG B 118 " pdb=" N TYR B 119 " pdb=" CA TYR B 119 " ideal model delta harmonic sigma weight residual -180.00 -154.83 -25.17 0 5.00e+00 4.00e-02 2.53e+01 dihedral pdb=" CA ARG A 118 " pdb=" C ARG A 118 " pdb=" N TYR A 119 " pdb=" CA TYR A 119 " ideal model delta harmonic sigma weight residual 180.00 -154.84 -25.16 0 5.00e+00 4.00e-02 2.53e+01 ... (remaining 8912 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.065: 1697 0.065 - 0.131: 367 0.131 - 0.196: 31 0.196 - 0.261: 15 0.261 - 0.326: 10 Chirality restraints: 2120 Sorted by residual: chirality pdb=" CG LEU C 246 " pdb=" CB LEU C 246 " pdb=" CD1 LEU C 246 " pdb=" CD2 LEU C 246 " both_signs ideal model delta sigma weight residual False -2.59 -2.26 -0.33 2.00e-01 2.50e+01 2.66e+00 chirality pdb=" CG LEU B 246 " pdb=" CB LEU B 246 " pdb=" CD1 LEU B 246 " pdb=" CD2 LEU B 246 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.62e+00 chirality pdb=" CG LEU D 246 " pdb=" CB LEU D 246 " pdb=" CD1 LEU D 246 " pdb=" CD2 LEU D 246 " both_signs ideal model delta sigma weight residual False -2.59 -2.27 -0.32 2.00e-01 2.50e+01 2.62e+00 ... (remaining 2117 not shown) Planarity restraints: 2320 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA BARG A 293 " 0.026 2.00e-02 2.50e+03 5.15e-02 2.65e+01 pdb=" C BARG A 293 " -0.089 2.00e-02 2.50e+03 pdb=" O BARG A 293 " 0.033 2.00e-02 2.50e+03 pdb=" N ALA A 294 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA AARG C 293 " 0.023 2.00e-02 2.50e+03 4.64e-02 2.15e+01 pdb=" C AARG C 293 " -0.080 2.00e-02 2.50e+03 pdb=" O AARG C 293 " 0.030 2.00e-02 2.50e+03 pdb=" N ALA C 294 " 0.027 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP E 72 " 0.001 2.00e-02 2.50e+03 2.87e-02 2.06e+01 pdb=" CG TRP E 72 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP E 72 " -0.002 2.00e-02 2.50e+03 pdb=" CD2 TRP E 72 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP E 72 " 0.025 2.00e-02 2.50e+03 pdb=" CE2 TRP E 72 " -0.032 2.00e-02 2.50e+03 pdb=" CE3 TRP E 72 " 0.019 2.00e-02 2.50e+03 pdb=" CZ2 TRP E 72 " 0.042 2.00e-02 2.50e+03 pdb=" CZ3 TRP E 72 " 0.027 2.00e-02 2.50e+03 pdb=" CH2 TRP E 72 " -0.058 2.00e-02 2.50e+03 ... (remaining 2317 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 2563 2.77 - 3.31: 12623 3.31 - 3.84: 22347 3.84 - 4.37: 27895 4.37 - 4.90: 47958 Nonbonded interactions: 113386 Sorted by model distance: nonbonded pdb=" O ASP A 115 " pdb=" O HOH A 501 " model vdw 2.243 3.040 nonbonded pdb=" O ASP B 115 " pdb=" O HOH B 501 " model vdw 2.250 3.040 nonbonded pdb=" O ASP C 115 " pdb=" O HOH C 501 " model vdw 2.250 3.040 nonbonded pdb=" O ASP E 115 " pdb=" O HOH E 501 " model vdw 2.251 3.040 nonbonded pdb=" O ASP D 115 " pdb=" O HOH D 501 " model vdw 2.251 3.040 ... (remaining 113381 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.05 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or resid 407 or (resid 408 and (name N or name C1 or name C10 or name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or na \ me C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P or \ name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 40 \ 9 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or n \ ame C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )))) selection = (chain 'B' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or name C1 or name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P o \ r name O5 or name P )) or (resid 408 and (name N or name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P o \ r name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 4 \ 09 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or \ name C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1 \ P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O \ 5 or name P )))) selection = (chain 'C' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or resid 407 or (resid 408 and (name N or name C1 or name C10 or name C \ 11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or na \ me C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P or \ name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 40 \ 9 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or name \ C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or n \ ame C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 o \ r name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1P \ or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 \ or name P )))) selection = (chain 'D' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or name C1 or name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P o \ r name O5 or name P )) or (resid 408 and (name N or name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P o \ r name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 4 \ 09 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or \ name C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1 \ P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O \ 5 or name P )))) selection = (chain 'E' and (resid 5 through 292 or resid 294 through 316 or (resid 403 throu \ gh 404 and (name C1 or name C10 or name C11 or name C12 or name C13 or name C14 \ or name C15 or name C16 or name C2 or name C3 or name C30 or name C31 or name C3 \ 2 or name C33 or name C34 or name C35 or name C36 or name O1P or name O2 or name \ O2P or name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (r \ esid 405 through 406 and (name C1 or name C10 or name C11 or name C12 or name C1 \ 3 or name C14 or name C15 or name C16 or name C17 or name C18 or name C19 or nam \ e C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name O1P or n \ ame O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O5 or n \ ame P )) or (resid 407 and (name N or name C1 or name C10 or name C11 or name C1 \ 2 or name C13 or name C14 or name C15 or name C16 or name C17 or name C2 or name \ C3 or name C30 or name C31 or name C32 or name C33 or name C34 or name C35 or n \ ame C36 or name C37 or name C38 or name C39 or name C4 or name C40 or name C5 or \ name O1P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P o \ r name O5 or name P )) or (resid 408 and (name N or name C1 or name C10 or name \ C11 or name C12 or name C13 or name C14 or name C15 or name C16 or name C17 or n \ ame C2 or name C3 or name C30 or name C31 or name C32 or name C33 or name C34 or \ name C35 or name C36 or name C4 or name C5 or name O1P or name O2 or name O2P o \ r name O3 or name O3P or name O4 or name O4P or name O5 or name P )) or (resid 4 \ 09 and (name N or name C1 or name C10 or name C11 or name C12 or name C13 or nam \ e C14 or name C15 or name C16 or name C17 or name C18 or name C19 or name C2 or \ name C20 or name C21 or name C22 or name C3 or name C30 or name C31 or name C32 \ or name C33 or name C34 or name C35 or name C36 or name C4 or name C5 or name O1 \ P or name O2 or name O2P or name O3 or name O3P or name O4 or name O4P or name O \ 5 or name P )))) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.47 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.920 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.610 Check model and map are aligned: 0.110 Set scattering table: 0.140 Process input model: 40.200 Find NCS groups from input model: 0.850 Set up NCS constraints: 0.100 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:13.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 14410 Z= 0.209 Angle : 0.885 9.728 19400 Z= 0.454 Chirality : 0.058 0.326 2120 Planarity : 0.010 0.063 2320 Dihedral : 23.408 161.701 5855 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 13.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.58 % Favored : 95.42 % Rotamer: Outliers : 0.36 % Allowed : 18.08 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.37 (0.20), residues: 1565 helix: 0.70 (0.21), residues: 495 sheet: -0.69 (0.27), residues: 355 loop : -2.24 (0.21), residues: 715 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.058 0.012 TRP E 72 HIS 0.003 0.001 HIS B 127 PHE 0.034 0.006 PHE E 210 TYR 0.054 0.007 TYR A 221 ARG 0.027 0.003 ARG B 58 Details of bonding type rmsd hydrogen bonds : bond 0.17027 ( 595) hydrogen bonds : angle 7.64205 ( 1985) covalent geometry : bond 0.00486 (14410) covalent geometry : angle 0.88526 (19400) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 1.523 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 42 PHE cc_start: 0.7947 (m-80) cc_final: 0.7713 (m-80) REVERT: B 47 TRP cc_start: 0.7401 (p90) cc_final: 0.7130 (p90) REVERT: B 245 ASN cc_start: 0.8116 (p0) cc_final: 0.7900 (p0) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 1.2037 time to fit residues: 90.5622 Evaluate side-chains 65 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 130 optimal weight: 0.4980 chunk 117 optimal weight: 4.9990 chunk 65 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 79 optimal weight: 9.9990 chunk 62 optimal weight: 20.0000 chunk 121 optimal weight: 5.9990 chunk 47 optimal weight: 0.0870 chunk 73 optimal weight: 4.9990 chunk 90 optimal weight: 5.9990 chunk 140 optimal weight: 2.9990 overall best weight: 2.7164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN C 200 ASN D 200 ASN B 200 ASN E 152 ASN E 200 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4265 r_free = 0.4265 target = 0.183152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.116570 restraints weight = 49455.068| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 3.53 r_work: 0.3135 rms_B_bonded: 4.44 restraints_weight: 0.5000 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3155 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3155 r_free = 0.3155 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3154 r_free = 0.3154 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3154 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.1140 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 14410 Z= 0.211 Angle : 0.709 7.077 19400 Z= 0.348 Chirality : 0.048 0.189 2120 Planarity : 0.006 0.051 2320 Dihedral : 25.597 169.524 2910 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 2.63 % Allowed : 15.30 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.21), residues: 1565 helix: 2.45 (0.21), residues: 495 sheet: -0.57 (0.25), residues: 415 loop : -1.50 (0.23), residues: 655 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 72 HIS 0.004 0.002 HIS D 235 PHE 0.018 0.002 PHE E 195 TYR 0.029 0.003 TYR A 102 ARG 0.004 0.001 ARG B 133 Details of bonding type rmsd hydrogen bonds : bond 0.08119 ( 595) hydrogen bonds : angle 4.93748 ( 1985) covalent geometry : bond 0.00515 (14410) covalent geometry : angle 0.70855 (19400) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 87 time to evaluate : 1.672 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 38 LYS cc_start: 0.8830 (mtpt) cc_final: 0.8576 (mtpt) REVERT: A 246 LEU cc_start: 0.7213 (OUTLIER) cc_final: 0.6815 (mt) REVERT: C 42 PHE cc_start: 0.8264 (m-80) cc_final: 0.7955 (m-80) REVERT: C 252 MET cc_start: 0.7114 (pmm) cc_final: 0.6817 (pmm) REVERT: B 47 TRP cc_start: 0.7748 (p90) cc_final: 0.7543 (p90) outliers start: 32 outliers final: 6 residues processed: 107 average time/residue: 0.8677 time to fit residues: 107.6349 Evaluate side-chains 84 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 77 time to evaluate : 1.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 246 LEU Chi-restraints excluded: chain D residue 26 GLU Chi-restraints excluded: chain B residue 26 GLU Chi-restraints excluded: chain E residue 26 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 147 optimal weight: 3.9990 chunk 70 optimal weight: 9.9990 chunk 131 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 107 optimal weight: 8.9990 chunk 140 optimal weight: 9.9990 chunk 115 optimal weight: 0.9980 chunk 106 optimal weight: 3.9990 chunk 118 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 89 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 83 ASN E 152 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.181392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.114766 restraints weight = 53918.437| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 3.63 r_work: 0.3079 rms_B_bonded: 4.56 restraints_weight: 0.5000 r_work (final): 0.3079 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3099 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3099 r_free = 0.3099 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3099 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8658 moved from start: 0.1614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14410 Z= 0.242 Angle : 0.726 10.040 19400 Z= 0.356 Chirality : 0.049 0.236 2120 Planarity : 0.006 0.052 2320 Dihedral : 23.321 175.560 2910 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.74 % Favored : 96.26 % Rotamer: Outliers : 2.49 % Allowed : 15.52 % Favored : 81.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.21), residues: 1565 helix: 2.67 (0.21), residues: 495 sheet: -0.43 (0.24), residues: 425 loop : -1.51 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 72 HIS 0.005 0.002 HIS D 127 PHE 0.021 0.002 PHE E 195 TYR 0.025 0.002 TYR E 102 ARG 0.004 0.001 ARG C 85 Details of bonding type rmsd hydrogen bonds : bond 0.08896 ( 595) hydrogen bonds : angle 4.70999 ( 1985) covalent geometry : bond 0.00603 (14410) covalent geometry : angle 0.72579 (19400) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 84 time to evaluate : 1.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 249 THR cc_start: 0.9019 (OUTLIER) cc_final: 0.8675 (t) REVERT: C 252 MET cc_start: 0.7016 (pmm) cc_final: 0.6763 (pmm) outliers start: 30 outliers final: 17 residues processed: 103 average time/residue: 0.8873 time to fit residues: 105.0746 Evaluate side-chains 95 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 77 time to evaluate : 1.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain C residue 249 THR Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 26 GLU Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 118 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 140 optimal weight: 5.9990 chunk 147 optimal weight: 2.9990 chunk 102 optimal weight: 9.9990 chunk 153 optimal weight: 0.6980 chunk 126 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 chunk 135 optimal weight: 4.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 19 ASN C 19 ASN B 19 ASN B 83 ASN E 152 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.184934 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.118218 restraints weight = 57342.015| |-----------------------------------------------------------------------------| r_work (start): 0.3383 rms_B_bonded: 3.80 r_work: 0.3151 rms_B_bonded: 4.64 restraints_weight: 0.5000 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3185 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3185 r_free = 0.3185 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3185 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14410 Z= 0.135 Angle : 0.643 12.944 19400 Z= 0.311 Chirality : 0.045 0.221 2120 Planarity : 0.005 0.047 2320 Dihedral : 21.972 179.225 2910 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.19 % Favored : 97.81 % Rotamer: Outliers : 2.14 % Allowed : 16.01 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1565 helix: 3.23 (0.21), residues: 495 sheet: -0.19 (0.24), residues: 425 loop : -1.33 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 72 HIS 0.003 0.001 HIS D 235 PHE 0.011 0.001 PHE C 37 TYR 0.022 0.002 TYR C 102 ARG 0.002 0.000 ARG C 58 Details of bonding type rmsd hydrogen bonds : bond 0.06201 ( 595) hydrogen bonds : angle 4.19289 ( 1985) covalent geometry : bond 0.00311 (14410) covalent geometry : angle 0.64272 (19400) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 88 time to evaluate : 1.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7175 (pmm) cc_final: 0.6960 (pmm) REVERT: D 249 THR cc_start: 0.8946 (p) cc_final: 0.8669 (t) outliers start: 25 outliers final: 10 residues processed: 101 average time/residue: 0.9617 time to fit residues: 110.7403 Evaluate side-chains 91 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 81 time to evaluate : 1.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 39 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 39 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 64 optimal weight: 0.0570 chunk 79 optimal weight: 0.7980 chunk 115 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 3 optimal weight: 0.8980 chunk 94 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 82 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 112 optimal weight: 5.9990 chunk 131 optimal weight: 4.9990 overall best weight: 1.7502 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 83 ASN D 19 ASN E 19 ASN E 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4277 r_free = 0.4277 target = 0.184487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3636 r_free = 0.3636 target = 0.117610 restraints weight = 56752.349| |-----------------------------------------------------------------------------| r_work (start): 0.3362 rms_B_bonded: 3.72 r_work: 0.3133 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3133 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3075 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3075 r_free = 0.3075 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3075 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.1853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14410 Z= 0.154 Angle : 0.644 9.410 19400 Z= 0.312 Chirality : 0.045 0.174 2120 Planarity : 0.005 0.045 2320 Dihedral : 21.527 179.515 2910 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.14 % Allowed : 16.23 % Favored : 81.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.75 (0.21), residues: 1565 helix: 3.28 (0.20), residues: 495 sheet: -0.17 (0.24), residues: 425 loop : -1.33 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 72 HIS 0.004 0.002 HIS E 235 PHE 0.014 0.001 PHE E 195 TYR 0.020 0.002 TYR B 102 ARG 0.003 0.000 ARG A 85 Details of bonding type rmsd hydrogen bonds : bond 0.06931 ( 595) hydrogen bonds : angle 4.20211 ( 1985) covalent geometry : bond 0.00370 (14410) covalent geometry : angle 0.64436 (19400) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 89 time to evaluate : 1.338 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 8 residues processed: 104 average time/residue: 0.8512 time to fit residues: 102.1922 Evaluate side-chains 87 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 79 time to evaluate : 1.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 GLU Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 39 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 61 optimal weight: 2.9990 chunk 17 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 99 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 106 optimal weight: 7.9990 chunk 135 optimal weight: 0.8980 chunk 67 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 0.8980 chunk 95 optimal weight: 6.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4283 r_free = 0.4283 target = 0.185055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3643 r_free = 0.3643 target = 0.118121 restraints weight = 53190.671| |-----------------------------------------------------------------------------| r_work (start): 0.3384 rms_B_bonded: 3.68 r_work: 0.3158 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3101 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.42 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3101 r_free = 0.3101 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3101 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14410 Z= 0.134 Angle : 0.620 8.757 19400 Z= 0.299 Chirality : 0.045 0.193 2120 Planarity : 0.005 0.044 2320 Dihedral : 20.907 179.954 2910 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.49 % Allowed : 15.59 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.21), residues: 1565 helix: 3.40 (0.20), residues: 495 sheet: -0.07 (0.23), residues: 425 loop : -1.28 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 72 HIS 0.003 0.001 HIS C 235 PHE 0.012 0.001 PHE C 37 TYR 0.019 0.002 TYR C 102 ARG 0.002 0.000 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.06150 ( 595) hydrogen bonds : angle 4.06842 ( 1985) covalent geometry : bond 0.00315 (14410) covalent geometry : angle 0.62048 (19400) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 79 time to evaluate : 1.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 92 ILE cc_start: 0.6840 (OUTLIER) cc_final: 0.6431 (mp) outliers start: 30 outliers final: 12 residues processed: 100 average time/residue: 1.1268 time to fit residues: 129.7631 Evaluate side-chains 87 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 261 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 152 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 13 optimal weight: 10.0000 chunk 3 optimal weight: 0.9980 chunk 140 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 150 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 114 optimal weight: 0.6980 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4303 r_free = 0.4303 target = 0.187199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.120119 restraints weight = 66679.207| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 4.07 r_work: 0.3180 rms_B_bonded: 4.83 restraints_weight: 0.5000 r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3215 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3215 r_free = 0.3215 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3215 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14410 Z= 0.113 Angle : 0.599 8.973 19400 Z= 0.287 Chirality : 0.044 0.174 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.192 179.259 2910 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 2.49 % Allowed : 15.44 % Favored : 82.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.04 (0.21), residues: 1565 helix: 3.60 (0.20), residues: 495 sheet: 0.04 (0.23), residues: 425 loop : -1.26 (0.24), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 72 HIS 0.002 0.001 HIS C 277 PHE 0.014 0.001 PHE E 42 TYR 0.018 0.001 TYR D 102 ARG 0.001 0.000 ARG D 133 Details of bonding type rmsd hydrogen bonds : bond 0.05165 ( 595) hydrogen bonds : angle 3.88369 ( 1985) covalent geometry : bond 0.00256 (14410) covalent geometry : angle 0.59907 (19400) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.484 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 67 GLU cc_start: 0.6328 (mp0) cc_final: 0.6094 (mp0) REVERT: C 40 ASN cc_start: 0.8102 (t0) cc_final: 0.7854 (m-40) REVERT: C 252 MET cc_start: 0.7454 (pmm) cc_final: 0.7122 (pmm) REVERT: D 76 ILE cc_start: 0.8705 (OUTLIER) cc_final: 0.8491 (mp) REVERT: E 92 ILE cc_start: 0.6802 (OUTLIER) cc_final: 0.6392 (mp) outliers start: 30 outliers final: 14 residues processed: 93 average time/residue: 1.8596 time to fit residues: 198.4825 Evaluate side-chains 83 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 67 time to evaluate : 1.730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 20 THR Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 76 ILE Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 39 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 261 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 81 optimal weight: 2.9990 chunk 129 optimal weight: 50.0000 chunk 74 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 35 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 134 optimal weight: 6.9990 chunk 31 optimal weight: 10.0000 chunk 145 optimal weight: 0.0980 chunk 119 optimal weight: 4.9990 overall best weight: 2.4188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4260 r_free = 0.4260 target = 0.182845 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.115864 restraints weight = 53414.026| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 3.68 r_work: 0.3113 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.2104 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 14410 Z= 0.182 Angle : 0.656 10.416 19400 Z= 0.317 Chirality : 0.046 0.226 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.512 179.947 2910 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.21 % Allowed : 15.44 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.83 (0.21), residues: 1565 helix: 3.31 (0.20), residues: 495 sheet: -0.02 (0.23), residues: 425 loop : -1.33 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 72 HIS 0.005 0.002 HIS C 235 PHE 0.016 0.002 PHE E 195 TYR 0.017 0.002 TYR B 102 ARG 0.005 0.000 ARG D 51 Details of bonding type rmsd hydrogen bonds : bond 0.07645 ( 595) hydrogen bonds : angle 4.20671 ( 1985) covalent geometry : bond 0.00448 (14410) covalent geometry : angle 0.65645 (19400) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7332 (pmm) cc_final: 0.6910 (pmm) REVERT: B 205 MET cc_start: 0.8278 (tpt) cc_final: 0.7444 (ttt) REVERT: E 92 ILE cc_start: 0.6735 (OUTLIER) cc_final: 0.6378 (mp) outliers start: 26 outliers final: 17 residues processed: 95 average time/residue: 1.0670 time to fit residues: 115.8957 Evaluate side-chains 89 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 71 time to evaluate : 1.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 2 optimal weight: 7.9990 chunk 145 optimal weight: 0.9990 chunk 55 optimal weight: 0.7980 chunk 108 optimal weight: 4.9990 chunk 129 optimal weight: 5.9990 chunk 84 optimal weight: 2.9990 chunk 68 optimal weight: 9.9990 chunk 128 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 77 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 83 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.184302 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.117476 restraints weight = 53972.435| |-----------------------------------------------------------------------------| r_work (start): 0.3371 rms_B_bonded: 3.72 r_work: 0.3145 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3145 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3181 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3181 r_free = 0.3181 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3181 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8598 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14410 Z= 0.142 Angle : 0.629 9.792 19400 Z= 0.302 Chirality : 0.045 0.195 2120 Planarity : 0.005 0.043 2320 Dihedral : 20.307 179.985 2910 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 1.92 % Allowed : 15.73 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.91 (0.21), residues: 1565 helix: 3.43 (0.20), residues: 495 sheet: 0.04 (0.23), residues: 425 loop : -1.35 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 72 HIS 0.003 0.001 HIS C 235 PHE 0.014 0.001 PHE B 42 TYR 0.018 0.002 TYR B 102 ARG 0.002 0.000 ARG D 85 Details of bonding type rmsd hydrogen bonds : bond 0.06543 ( 595) hydrogen bonds : angle 4.07612 ( 1985) covalent geometry : bond 0.00338 (14410) covalent geometry : angle 0.62910 (19400) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 74 time to evaluate : 1.543 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7380 (pmm) cc_final: 0.7042 (pmm) REVERT: B 205 MET cc_start: 0.8267 (tpt) cc_final: 0.7483 (ttt) REVERT: E 92 ILE cc_start: 0.6931 (OUTLIER) cc_final: 0.6528 (mp) outliers start: 22 outliers final: 16 residues processed: 93 average time/residue: 0.9135 time to fit residues: 97.6873 Evaluate side-chains 87 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 1.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain A residue 261 MET Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 138 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 141 optimal weight: 7.9990 chunk 65 optimal weight: 9.9990 chunk 116 optimal weight: 4.9990 chunk 103 optimal weight: 0.0670 chunk 48 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 75 optimal weight: 20.0000 chunk 84 optimal weight: 2.9990 overall best weight: 2.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.182340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.114942 restraints weight = 66705.897| |-----------------------------------------------------------------------------| r_work (start): 0.3321 rms_B_bonded: 4.01 r_work: 0.3074 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3024 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.40 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8655 moved from start: 0.2224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 14410 Z= 0.196 Angle : 0.682 11.136 19400 Z= 0.329 Chirality : 0.047 0.223 2120 Planarity : 0.005 0.044 2320 Dihedral : 20.525 179.929 2910 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 1.78 % Allowed : 16.01 % Favored : 82.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.72 (0.21), residues: 1565 helix: 3.24 (0.20), residues: 495 sheet: -0.04 (0.23), residues: 425 loop : -1.45 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP D 72 HIS 0.006 0.002 HIS C 235 PHE 0.016 0.002 PHE E 195 TYR 0.017 0.002 TYR C 102 ARG 0.004 0.001 ARG E 85 Details of bonding type rmsd hydrogen bonds : bond 0.07891 ( 595) hydrogen bonds : angle 4.26630 ( 1985) covalent geometry : bond 0.00488 (14410) covalent geometry : angle 0.68175 (19400) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3130 Ramachandran restraints generated. 1565 Oldfield, 0 Emsley, 1565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 1.480 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 252 MET cc_start: 0.7317 (pmm) cc_final: 0.6962 (pmm) REVERT: B 205 MET cc_start: 0.8371 (tpt) cc_final: 0.7558 (ttt) REVERT: E 92 ILE cc_start: 0.6793 (OUTLIER) cc_final: 0.6411 (mp) outliers start: 20 outliers final: 16 residues processed: 89 average time/residue: 0.9555 time to fit residues: 98.1143 Evaluate side-chains 88 residues out of total 1395 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 71 time to evaluate : 1.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 VAL Chi-restraints excluded: chain A residue 92 ILE Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 242 VAL Chi-restraints excluded: chain C residue 26 GLU Chi-restraints excluded: chain C residue 39 VAL Chi-restraints excluded: chain C residue 92 ILE Chi-restraints excluded: chain C residue 141 VAL Chi-restraints excluded: chain C residue 242 VAL Chi-restraints excluded: chain D residue 39 VAL Chi-restraints excluded: chain D residue 92 ILE Chi-restraints excluded: chain D residue 242 VAL Chi-restraints excluded: chain D residue 261 MET Chi-restraints excluded: chain B residue 92 ILE Chi-restraints excluded: chain B residue 242 VAL Chi-restraints excluded: chain E residue 92 ILE Chi-restraints excluded: chain E residue 242 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 155 random chunks: chunk 94 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 129 optimal weight: 7.9990 chunk 108 optimal weight: 5.9990 chunk 86 optimal weight: 0.4980 chunk 131 optimal weight: 0.0670 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 121 optimal weight: 4.9990 chunk 40 optimal weight: 8.9990 overall best weight: 1.4120 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.184540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3641 r_free = 0.3641 target = 0.117958 restraints weight = 54470.092| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.71 r_work: 0.3073 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3178 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3178 r_free = 0.3178 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.41 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3178 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8570 moved from start: 0.2248 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14410 Z= 0.138 Angle : 0.640 10.076 19400 Z= 0.307 Chirality : 0.045 0.175 2120 Planarity : 0.005 0.042 2320 Dihedral : 20.207 179.492 2910 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 5.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.64 % Allowed : 16.01 % Favored : 82.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.21), residues: 1565 helix: 3.46 (0.20), residues: 495 sheet: 0.09 (0.23), residues: 425 loop : -1.39 (0.23), residues: 645 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 72 HIS 0.003 0.001 HIS C 235 PHE 0.016 0.001 PHE A 42 TYR 0.018 0.002 TYR D 102 ARG 0.004 0.000 ARG E 133 Details of bonding type rmsd hydrogen bonds : bond 0.06343 ( 595) hydrogen bonds : angle 4.05687 ( 1985) covalent geometry : bond 0.00330 (14410) covalent geometry : angle 0.64039 (19400) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9855.47 seconds wall clock time: 173 minutes 15.11 seconds (10395.11 seconds total)